Examples of org.apache.commons.cli.HelpFormatter

org.apache.commons.cli.HelpFormatter
A formatter of help messages for the current command line options @author Slawek Zachcial @author John Keyes (john at integralsource.com)

      }
  }


    private static void printCliHelp(Options cliOptions)
    {
      HelpFormatter helpFormatter = new HelpFormatter();
      helpFormatter.printHelp("java " + BootstrapSeederMain.class.getName(), cliOptions);
    }

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  }


    private static void printCliHelp(Options cliOptions)
    {
      HelpFormatter helpFormatter = new HelpFormatter();
      helpFormatter.printHelp("java " + BootstrapSeederMain.class.getName(), cliOptions);
    }

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    }
  }


  private static void printCliHelp(Options cliOptions)
  {
    HelpFormatter helpFormatter = new HelpFormatter();
    helpFormatter.printHelp("java " + BootstrapSeederMain.class.getName(), cliOptions);
  }

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    }
  }


  private static void printCliHelp(Options cliOptions)
  {
    HelpFormatter helpFormatter = new HelpFormatter();
    helpFormatter.printHelp("java " + BootstrapDBCleanerMain.class.getName(), cliOptions);
  }

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                    throw new IllegalArgumentException(gene + " is NOT valid, only allows " + ClassifierFactory.RRNA_16S_GENE + " and " + ClassifierFactory.FUNGALLSU_GENE);
                }
            }
        } catch (Exception e) {
            System.out.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(120, "ComparisonCmd", "", options, "", true);
            return;
        }


        if (propFile == null && gene == null) {
            gene = ClassifierFactory.RRNA_16S_GENE;

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        options.addOption("S", "significance", false, "Compute significance with unifrac metric");
        options.addOption("o", "outfile", true, "Write results to file instead of stdout");
    }


    private static void printUsage() {
        new HelpFormatter().printHelp("Unifrac", options, true);
    }

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            }
            queryFile = args[0];
            
        } catch (Exception e) {
            System.out.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(120, "ClassifierCmd [options] <samplefile>\nNote this is the legacy command for one sample classification ", "", options, "");


            return;
        }


        if (propFile == null && gene == null) {

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            if (samples.size() < 1) {
                throw new IllegalArgumentException("Require at least one sample files");
            }
        }catch (Exception e) {
            System.out.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(80, " [options] <samplefile>[,idmappingfile] ...", "", options, "");
            return;
        }
        
        MultiClassifier multiClassifier = new MultiClassifier(propFile, gene, biomFile, metadataFile);
        MultiClassifierResult result = multiClassifier.multiCompare(samples, conf, assign_out, format, min_bootstrap_words);

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                modification = line.getOptionValue("m");
            }
            
        } catch (Exception e) {
            System.out.println("Command Error: " + e.getMessage());
            new HelpFormatter().printHelp(120, "train", "", options, "", true);
            return;
        }
        
        ClassifierTraineeMaker maker = new ClassifierTraineeMaker(taxFile, seqFile, cnFile, trainset_no, version, modification, outdir);
    }

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      CommandLineParser parser = new GnuParser();
      CommandLine commandLine = parser.parse(options, args);


      if (commandLine.hasOption('h')) {
        new HelpFormatter().printHelp("flume-ng agent", options, true);
        return;
      }


      String agentName = commandLine.getOptionValue('n');
      boolean reload = !commandLine.hasOption("no-reload-conf");

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